Molecular footprint of drug-selective pressure in a human immunodeficiency virus transmission chain

Known human immunodeficiency virus (HIV) transmission histories are invaluable models for investigating the evolutionary and transmission dynamics of the virus and to assess the accuracy of phylogenetic reconstructions. Here we have characterized an HIV-1 transmission chain consisting of nine infected patients, almost all of whom were treated with antiviral drugs at later stages of infection. Partial pol and env gp41 regions of the HIV genome were directly sequenced from plasma viral RNA for at least one sample from each patient. Phylogenetic analyses in pol using likelihood methods inferred an evolutionary history not fully compatible with the known transmission history. This could be attributed to parallel evolution of drug resistance mutations resulting in the incorrect clustering of multidrug-resistant virus. On the other hand, a fully compatible phylogenetic tree was reconstructed from the env sequences. We were able to identify and quantify the molecular footprint of drug-selective pressure in pol using maximum likelihood inference under different codon substitution models. An increased fixation rate of mutations in the HIV population of the multidrug-resistant patient was demonstrated using molecular clock modeling. We show that molecular evolutionary analyses, guided by a known transmission history, can reveal the presence of confounding factors like natural selection and caution should be taken when accurate descriptions of HIV evolution are required.status: publishe

The domestication of the probiotic bacterium Lactobacillus acidophilus

Lactobacillus acidophilus is a Gram-positive lactic acid bacterium that has had widespread historical use in the dairy industry and more recently as a probiotic. Although L. acidophilus has been designated as safe for human consumption, increasing commercial regulation and clinical demands for probiotic validation has resulted in a need to understand its genetic diversity. By drawing on large, well-characterised collections of lactic acid bacteria, we examined L. acidophilus isolates spanning 92 years and including multiple strains in current commercial use. Analysis of the whole genome sequence data set (34 isolate genomes) demonstrated L. acidophilus was a low diversity, monophyletic species with commercial isolates essentially identical at the sequence level. Our results indicate that commercial use has domesticated L. acidophilus with genetically stable, invariant strains being consumed globally by the human population

Equality, value pluralism and relevance: Is luck egalitarianism in one way good, but not all things considered?

Some luck egalitarians argue that justice is just one value among others and is thus not necessarily what we should strive for in order to make the world better. Yet, by focusing on only one dimension of what matters – luck equality – it proves very difficult to draw political implications in cases where several values are in tension. We believe that normative political philosophy must have the ambitionto guide political action. Hence, in this paper we make a negative and a positive point. Negatively, we argue that the inability to offer recommendations on what to strive for potentially weakens Kasper Lippert-Rasmussen’s account of luck egalitarianism. In order not to be irrelevant for political practice, a more serviceable version of luck egalitarianism that would allow for all-things-considered judgments is needed. Positively, we examine two possible routes toward such a view. One would be to stick to pluralism, but to discuss possible clashes and find a rule of regulation in each case. Another would consist in giving up value pluralism by identifying an over-arching value or principle that would arbitrate between different values. We suggest that Lippert-Rasmussen’s foundation of equality carries the potential for such an overarching principle.Political Philosophy and Ethic

Nutrient-Dense Orange-Fleshed Sweetpotato: Advances in Drought-Tolerance Breeding and Understanding of Management Practices for Sustainable Next-Generation Cropping Systems in Sub-Saharan Africa

Almost half of children < 5 years old living in sub-Saharan Africa (SSA) suffer from vitamin A deficiency and 60% suffer from iron deficiency. Thus, there has been a strong commitment to breeding for, promoting awareness of, and delivering adapted pro-vitamin A rich orange-fleshed sweetpotato (OFSP) in SSA during the past two decades and for enhanced iron content since 2014. This review article focuses on major breeding efforts in SSA to enhance the drought tolerance of OFSP and reviews integrated crop management practices for improved and sustained sweetpotato production in SSA farming systems. Under climate change, the frequency and severity of droughts is expected to increase. Technical issues are presented in the context of addressing challenges along the entire value chain to ensure adoption. First, the use of an accelerated breeding scheme reduced the breeding cycle from 8–10 to 4–5 years. Since 2010, 19 drought-tolerant OFSP cultivars have been released in Mozambique, 7 in Malawi, and 2 in South Africa. Moreover, research in four breeding populations using the heterosis exploiting breeding scheme (HEBS) demonstrated that within one breeding cycle of 5 years, clones with significantly higher root yield, abiotic tolerance, host plant resistance to pests and diseases, and early maturity can be produced. In the future, HEBS will be combined with greater use of modern genomic tools, new phenotyping tools, and CRISPR/Cas9-mediated gene editing. Second, beyond genetic enhancements, evidence is presented that using improved crop management systems, existing sweet potato yields can be increased 2–4 times. Current knowledge is reviewed concerning sweetpotato’s role in diverse farming systems, but integrated crop management is clearly under researched. Third, the outlook for drought tolerance breeding indicates that two distinct classes of nutrient-rich cultivars are emerging: (1) Early maturing cultivars (< 4 month growing period) that escape drought but also serve humid environments with small landholding size per capita; and (2) Medium maturing (4–6 month growing period) cultivars that avoid drought, are drought tolerant and exhibit continuous root formation. Increasing commercialization of the crop and climate change will drive demand, and the willingness of farmers to invest in improved sweetpotato crop management

Factors influencing adherence to antiretroviral therapy among people living with HIV in an urban and rural setting, Tanzania

Adherence is one of the most crucial determinants of treatment response to antiretroviral therapy (ART). An analytical cross-sectional study was conducted in 24 Care and Treatment Centres (CTC) in Dar es Salaam and Iringa regions in Tanzania. Data was collected using questionnaire and appointments records. A total of 943 patients attending at the care and treatment sites in Dar es Salaam and Iringa were recruited. Adherence based on keeping appointments and on four days recall was 65% and 70%, respectively. Adherence based on taking ART more than 95% of the time in one month was 83%. Satisfaction with health services, having treatment support, having knowledge on the use of ART, early presentation to CTC, and being on ART for more than one year, were associated with good adherence. Being in the urban region, using traditional medicine, medicine side effects and alcohol consumption problems negatively associated with adherence to ART.Keywords: Adherence barriers, antiretroviral therapy, HIV, Tanzania, rural, urba

A 59-Year-Old Woman With Chronic Skin Lesions of the Leg

Diagnosis: Acrodermatitis chronica atrophicans